The above-ground section of the station is cross-shaped, with the Chūō-Sōbu Line tracks running from east to west, and the Yamanote and Keihin-Tohoku Line (and Tohoku Shinkansen, which does not stop at Akihabara) from north to south.

There are two island platforms serving four tracks for the Yamanote Line and the Keihin-Tohoku Line on the 2nd level, and two side platforms serving two tracks for the Sobu Line Local service on the 4th level.

Akihabara Station was opened in November 1890 as a freight terminal linked to Ueno Station station via tracks following the course of the modern day Yamanote Line.

It was opened to passenger traffic in 1925 following the construction of the section of track linking Ueno with Shinbashi via Tokyo Station and the completion of the Yamanote Line. The upper level platforms were added in 1932 with the opening of an extension to the Sōbu Line from its old terminal at Ryōgoku to Ochanomizu, making Akihabara an important transfer station for passengers from the east of Tokyo and Chiba Prefecture.

The huge growth in commuter traffic following the Second World War caused considerable congestion and was only relieved with the construction of the Sōbu line tunnel linking Kinshichō with Tokyo, bypassing Akihabara.

On August 24, 2005, the underground terminus of the new Tsukuba Express Line opened at Akihabara. The entire station complex, including the JR station, was also refurbished and enlarged in preparation for the opening of the Tsukuba Express.[3]

In fiscal 2013, the JR East station was used by an average of 240,327 passengers daily (boarding passengers only), making it the ninth-busiest station operated by JR East.[4] Over the same fiscal year, the Tokyo Metro station was used by an average of 122,576 passengers daily (both exiting and entering passengers), making it the 23rd busiest Tokyo Metro station.[5]